genoset 1.20.0
Peter M. Haverty
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/genoset | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ WARNINGS ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genoset_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/genoset.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genoset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoset’ version ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genoset’ can be installed ... [26s/29s] WARNING
Found the following significant warnings:
Warning: subclass "DelegatingGenomicRanges" of class "GenomicRanges" is not local and cannot be updated for new inheritance information; consider setClassUnion()
See ‘/Users/biocbuild/bbs-3.0-bioc/meat/genoset.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
.Call("RleViews_viewMaxs", ..., PACKAGE = "IRanges")
.Call("RleViews_viewMeans", ..., PACKAGE = "IRanges")
.Call("RleViews_viewMins", ..., PACKAGE = "IRanges")
.Call("RleViews_viewSums", ..., PACKAGE = "IRanges")
.Call("RleViews_viewWhichMaxs", ..., PACKAGE = "IRanges")
.Call("RleViews_viewWhichMins", ..., PACKAGE = "IRanges")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
calcGC : <anonymous>: no visible global function definition for ‘Views’
calcGC : <anonymous>: no visible global function definition for
‘alphabetFrequency’
initGenoSet: no visible global function definition for ‘universe<-’
initGenoSet: no visible global function definition for
‘assayDataValidMembers’
colnames<-,GenoSet: no visible global function definition for ‘pData’
colnames<-,GenoSet: no visible global function definition for ‘pData<-’
colnames<-,GenoSet: no visible global function definition for
‘assayData’
colnames<-,GenoSet: no visible global function definition for
‘assayData<-’
dim,GenoSet: no visible global function definition for ‘featureData’
rownames<-,GenoSet: no visible global function definition for ‘fData<-’
rownames<-,GenoSet: no visible global function definition for
‘assayData’
rownames<-,GenoSet: no visible global function definition for
‘assayData<-’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'colnames,GenoSet-method'
‘object’ ‘value’
Undocumented arguments in documentation object 'genome,GenoSet-method'
‘value’
Undocumented arguments in documentation object '[,GenoSet,ANY-method'
‘value’
Undocumented arguments in documentation object 'rownames,GRanges-method'
‘x’ ‘value’
Undocumented arguments in documentation object 'show,GenoSet-method'
‘object’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/18s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘prove.R’ [27s/25s]
Comparing ‘prove.Rout’ to ‘prove.Rout.save’ ...19,24c19,24
< anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
< do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
< is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
< pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
< rownames, sapply, setdiff, sort, table, tapply, union, unique,
< unlist, unsplit
---
> Filter, Find, Map, Position, Reduce, anyDuplicated, append,
> as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
> eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
> mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
> rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
> unique, unlist
31a32,39
>
> Attaching package: 'GenomicRanges'
>
> The following objects are masked from 'package:GenomeInfoDb':
>
> Seqinfo, dropSeqlevels, keepSeqlevels, keepStandardChromosomes,
> renameSeqlevels, restoreSeqlevels
>
51c59
< RUNIT TEST PROTOCOL -- Fri Apr 10 02:10:47 2015
---
> RUNIT TEST PROTOCOL -- Thu May 8 09:40:10 2014
53c61
< Number of test functions: 33
---
> Number of test functions: 30
59,60c67,68
< genoset RUnit Tests - 33 test functions, 0 errors, 0 failures
< Number of test functions: 33
---
> genoset RUnit Tests - 30 test functions, 0 errors, 0 failures
> Number of test functions: 30
63d70
< There were 16 warnings (use warnings() to see them)
[27s/26s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/genoset.Rcheck/00check.log’
for details.